Amplicon-based microbiome study highlights the loss of diversity and the establishment of a set of species in patients with dentin caries

HIV Infection and Exposure Increases Cariogenic Taxa, Reduces Taxonomic Turnover, and Homogenizes Spatial Differentiation for the Supragingival Microbiome

Background The oral microbiome comprises distinct microbial communities that colonize diverse ecological niches across the oral cavity, the composition of which are influenced by nutrient and substrate availability, host genetics, diet, behavior, age, and other diverse host and environmental factors. Unlike other densely populated human-associated microbial ecosystems (e.g., gut, urogenital), the oral microbiome is regularly and directly exposed to the external environment and is therefore likely less stable over time. Cross sectional studies of the oral microbiome capture a glimpse of this temporal dynamism, yet a full appreciation of the relative stability, robusticity, and spatial structure of the oral environment is necessary to understand the role of microbial communities in promoting health or disease. Results Here we investigate the spatial and temporal stability of the oral microbiome over three sampling time points in the context of HIV infection and exposure. Individual teeth were sampled from a cohort of 565 Nigerian children with varying levels of tooth decay severity (i.e., caries disease). We collected 1,960 supragingival plaque samples and characterized the oral microbiome using a metataxonomic approach targeting an approximately 478 bp region of the bacterial rpo C gene. We found that both infection and exposure to HIV have significant effects on the stability of the supragingival plaque microbiome at both the spatial and temporal scale. Specifically, we detect (1) significantly lower taxonomic turnover of the oral community among exposed and infected children compared to unexposed children, (2) we find that HIV infection homogenizes the oral community across the anterior and posterior dentition, and (3) that impaired immunity (i.e., low CD4 count) and low taxonomic turnover over time in children living with HIV is associated with higher frequency of cariogenic taxa including Streptococcus mutans . Conclusions Our results document substantial community fluctuations over time in children unexposed to HIV independent of oral health status. This suggests that the oral community, under typical conditions, rapidly adapts to environmental perturbations to maintain homeostasis and that long-term taxonomic rigidity is a signal of community dysfunction, potentially leading to a higher incidence of oral disease including caries.

Propolis as a functional food and promising agent for oral health and microbiota balance: A review study

Bee Propolis has been used for its therapeutic properties, including anti-inflammatory, antibacterial, antifungal, and immune-stimulating properties, for centuries as a functional food. This study reviewed the effectiveness of propolis as a functional food on oral-related diseases as a rich bioflavonoid produced by honey bees. A literature search was conducted to identify studies published that investigated the effects of propolis on oral health and its ability to treat related diseases. The search was performed in electronic databases using relevant keywords. Initially, 3429 studies were identified through database searching, and based on the inclusion and exclusion criteria, 22 articles were eligible to be included. Reviewing the articles, propolis was recognized as a functional food and promising agent to balance oral microbiota and prevent oral diseases due to its effectiveness on related bacteria, its anti-inflammatory properties, and its activity against Porphyromonas gingivalis and Actinomyces Oris allowed it to be an effective substance to prevent periodontal diseases. Based on our findings, Propolis is a desirable preventive option for various oral health conditions, including dental caries and periodontal diseases. Therefore, it is recommended to be consumed as a functional food in our daily diet, which can reduce the risk of oral disease and improve oral health.

Moderate-intensity continuous training and high-intensity interval training modulate the composition of the oral microbiota of elderly adults: Randomized controlled trial

OBJECTIVE

We investigates the effects of 16-week high-intensity interval training and moderate-intensity continuous training on the composition of the oral microbiota. To the best of our knowledge, at the time of writing this paper no other scholars had described the oral metagenomic changes associated with prescribed exercise in older adults.

METHODS

Forty-three participants aged 60-74 years were randomized 1:1:1 to a control group, high-intensity interval training or moderate-intensity continuous training twice weekly for 16 weeks. Saliva samples were sequenced at baseline, week 8 and week 16 of intervention.

RESULTS

High-intensity interval training produced significant differences over time in Richness and a clear trend to decreased Simpson and Shannon diversity indices. In contrast, Simpson and Shannon indices showed an upward trend over time with moderate-intensity continuous training, which also decreased Firmicutes and increased Bacteroidetes levels. Significant differences in the abundance of pathogenic species were also observed after the participants completed the exercise interventions of either type.

CONCLUSIONS

Both types of exercise promoted subtle changes in the oral microbiota, confirming the modulatory effect of high-intensity interval training and moderate-intensity continuous training on the oral microbiome. Clinical trial registration NCT05220670.

Where bacteria and eukaryotes meet

The international workshop "Interdisciplinary life of microbes: from single cells to multicellular aggregates," following a virtual preassembly in November 2021, was held in person in Dresden, from 9 to 13 November 2022. It attracted not only prominent experts in biofilm research but also researchers from broadly neighboring disciplines, such as medicine, chemistry, and theoretical and experimental biophysics, both eukaryotic and prokaryotic. Focused brainstorming sessions were the special feature of the event and are at the heart of this commentary.

Probiotics Partly Suppress the Impact of Sugar Stress on the Oral Microbiota-A Randomized, Double-Blinded, Placebo-Controlled Trial

The aim was to test if probiotics counteract oral dysbiosis during 14 days of sugar stress and subsequently help restore oral homeostasis. Eighty healthy individuals received either probiotics (n = 40) or placebo lozenges (n = 40) for 28 days and rinsed with a 10% sucrose solution 6-8 times during the initial 14 days of the trial. Saliva and supragingival samples were collected at baseline, day 14, and day 28. Saliva samples were analyzed for levels of pro-inflammatory cytokines, albumin, and salivary enzyme activity. The supragingival microbiota was characterized according to the Human Oral Microbiome Database. After 14 days of sugar stress, the relative abundance of Porphyromonas species was significantly higher (p = 0.03) and remained significantly elevated at day 28 in the probiotic group compared to the placebo group (p = 0.004). At day 28, the relative abundance of Kingella species was significantly higher in the probiotic group (p = 0.03). Streptococcus gordinii and Neisseria elongata were associated with the probiotic group on day 28, while Streptococcus sobrinus was associated with the placebo group on day 14 and day 28. On day 28, the salivary albumin level was significantly lower in the probiotic group. The present study demonstrates a potential stabilizing effect on the supragingival microbiota mediated by consumption of probiotics during short-term sugar stress.

The making of the oral microbiome in Agta hunter-gatherers

Ecological and genetic factors have influenced the composition of the human microbiome during our evolutionary history. We analysed the oral microbiota of the Agta, a hunter-gatherer population where some members have adopted an agricultural diet. We show that age is the strongest factor modulating the microbiome, probably through immunosenescence since we identified an increase in the number of species classified as pathogens with age. We also characterised biological and cultural processes generating sexual dimorphism in the oral microbiome. A small subset of oral bacteria is influenced by the host genome, linking host collagen genes to bacterial biofilm formation. Our data also suggest that shifting from a fish/meat diet to a rice-rich diet transforms their microbiome, mirroring the Neolithic transition. All of these factors have implications in the epidemiology of oral diseases. Thus, the human oral microbiome is multifactorial and shaped by various ecological and social factors that modify the oral environment.

The oral microbiota is a reservoir for antimicrobial resistance: resistome and phenotypic resistance characteristics of oral biofilm in health, caries, and periodontitis

BACKGROUND

Antimicrobial resistance (AMR) is an ever-growing threat to modern medicine and, according to the latest reports, it causes nearly twice as many deaths globally as AIDS or malaria. Elucidating reservoirs and dissemination routes of antimicrobial resistance genes (ARGs) are essential in fighting AMR. Human commensals represent an important reservoir, which is underexplored for the oral microbiota. Here, we set out to investigate the resistome and phenotypic resistance of oral biofilm microbiota from 179 orally healthy (H), caries active (C), and periodontally diseased (P) individuals (TRN: DRKS00013119, Registration date: 22.10.2022). The samples were analysed using shotgun metagenomic sequencing combined, for the first time, with culture technique. A selection of 997 isolates was tested for resistance to relevant antibiotics.

RESULTS

The shotgun metagenomics sequencing resulted in 2,069,295,923 reads classified into 4856 species-level OTUs. PERMANOVA analysis of beta-diversity revealed significant differences between the groups regarding their microbiota composition and their ARG profile. The samples were clustered into three ecotypes based on their microbial composition. The bacterial composition of H and C samples greatly overlapped and was based on ecotypes 1 and 2 whereas ecotype 3 was only detected in periodontitis. We found 64 ARGs conveying resistance to 36 antibiotics, particularly to tetracycline, macrolide-lincosamide-streptogramin, and beta-lactam antibiotics, and a correspondingly high prevalence of phenotypic resistance. Based on the microbiota composition, these ARGs cluster in different resistotypes, and a higher prevalence is found in healthy and caries active than in periodontally diseased individuals. There was a significant association between the resistotypes and the ecotypes. Although numerous associations were found between specific antibiotic resistance and bacterial taxa, only a few taxa showed matching associations with both genotypic and phenotypic analyses.

CONCLUSIONS

Our findings show the importance of the oral microbiota from different niches within the oral cavity as a reservoir for antibiotic resistance. Additionally, the present study showed the need for using more than one method to reveal antibiotic resistance within the total oral biofilm, as a clear mismatch between the shotgun metagenomics method and the phenotypic resistance characterization was shown.

Does fluoride exposure impact on the human microbiome?

Fluoride is added to drinking water in some countries to prevent tooth decay (caries). There is no conclusive evidence that community water fluoridation (CWF) at WHO recommended concentrations for caries prevention has any harmful effects. However, research is ongoing regarding potential effects of ingested fluoride on human neurodevelopment and endocrine dysfunction. Simultaneously, research has emerged highlighting the significance of the human microbiome in gastrointestinal and immune health. In this review we evaluate the literature examining the effect of fluoride exposure on the human microbiome. Unfortunately, none of the studies retrieved examined the effects of ingested fluoridated water on the human microbiome. Animal studies generally examined acute fluoride toxicity following ingestion of fluoridated food and water and conclude that fluoride exposure can detrimentally perturb the normal microbiome. These data are difficult to extrapolate to physiologically relevant human exposure dose ranges and the significance to humans living in areas with CWF requires further investigation. Conversely, evidence suggests that the use of fluoride containing oral hygiene products may have beneficial effects on the oral microbiome regarding caries prevention. Overall, while fluoride exposure does appear to impact the human and animal microbiome, the long-term consequences of this requires further study.

The role of the oral microbiome in smoking-related cardiovascular risk: a review of the literature exploring mechanisms and pathways

Cardiovascular disease is a leading cause of morbidity and mortality. Oral health is associated with smoking and cardiovascular outcomes, but there are gaps in knowledge of many mechanisms connecting smoking to cardiovascular risk. Therefore, the aim of this review is to synthesize literature on smoking and the oral microbiome, and smoking and cardiovascular risk/disease, respectively. A secondary aim is to identify common associations between the oral microbiome and cardiovascular risk/disease to smoking, respectively, to identify potential shared oral microbiome-associated mechanisms. We identified several oral bacteria across varying studies that were associated with smoking. Atopobium, Gemella, Megasphaera, Mycoplasma, Porphyromonas, Prevotella, Rothia, Treponema, and Veillonella were increased, while Bergeyella, Haemophilus, Lautropia, and Neisseria were decreased in the oral microbiome of smokers versus non-smokers. Several bacteria that were increased in the oral microbiome of smokers were also positively associated with cardiovascular outcomes including Porphyromonas, Prevotella, Treponema, and Veillonella. We review possible mechanisms that may link the oral microbiome to smoking and cardiovascular risk including inflammation, modulation of amino acids and lipids, and nitric oxide modulation. Our hope is this review will inform future research targeting the microbiome and smoking-related cardiovascular disease so possible microbial targets for cardiovascular risk reduction can be identified.

Overexpression of proinflammatory cytokines in dental pulp tissue and distinct bacterial microbiota in carious teeth of Mexican Individuals

The prevalence of dental caries in the Mexican adult population aged 20 to 85 years is around 93.3%, and 50% in Mexican children and adolescents. Worldwide, it is the most common non-communicable disease. One of the main etiological factors for dental caries is the oral microbiome and changes in its structure and function, with an expansion of pathogenic bacteria like Streptococcus mutans. The exposed dental pulp tissue triggers an innate immune response to counteract this bacterial invasion. The relation between oral dysbiosis and innate immune responses remains unclear. We aimed to understand the relationship between innate immune response and the oral microbiota by quantifying the expression of Toll-like receptors (TLRs) and proinflammatory markers (cytokines and a chemokine) in dental pulp tissue, either exposed or not to carious dentin, and to correlate this information with the oral microbiome found in healthy teeth and those with moderate caries. RNA was purified from pulp tissue, subjected to RT-qPCR and analysed with the ^ΔΔCt method. Supragingival dental plaque of non-carious teeth and dentin of carious teeth were subjected to 16S targeted sequencing. Principal coordinate analysis, permutational multivariate ANOVA, and linear discriminant analysis were used to assess differences between non-carious and carious teeth. Correlations were assessed with Spearman´s test and corrected for multiple comparisons using the FDR method. The relative abundance (RA) of Lactobacillus, Actinomyces, Prevotella, and Mitsuokella was increased in carious teeth; while the RA of Haemophilus and Porphyromonas decreased. Olsenella and Parascardovia were only detected in carious teeth. Significant overexpression of interleukin 1 beta (IL1 β), IL6, and CXCL8 was detected in pulp tissue exposed to carious dentin. IL1β correlated positively with TLR2 and Actinomyces; yet negatively with Porphyromonas. These findings suggest that immune response of pulp tissue chronically exposed to cariogenic microbiome is triggered by proinflammatory cytokines IL1β and IL6 and the chemokine CXCL8.

The Effect of Amino Sugars on the Composition and Metabolism of a Microcosm Biofilm and the Cariogenic Potential against Teeth and Dental Materials

Amino sugars N-acetylglucosamine (GlcNAc) and glucosamine (GlcN) are abundant sources of carbon and nitrogen in the oral cavity. The aim of this study was to investigate the effects of GlcNAc metabolism on the genomics and biochemistry of a saliva-derived microbial community, and on the surface integrity of human teeth and restorative surfaces. Pooled cell-containing saliva (CCS) was used to establish a microcosm biofilm in vitro in a biofilm medium (BM) containing 5 different carbohydrates. The microbial composition of each biofilm was analyzed by 16S rRNA amplicon sequencing, and the concentrations of eight organic acids were determined for selected sugars by targeted metabolomics. Meanwhile, extracted human teeth and polished titanium and ceramic disks were submerged in BM supplemented with 1% of glucose or GlcNAc, inoculated with CCS and Streptococcus mutans UA159, and incubated for 30 days. To mimic the effects of other microbial byproducts, the specimens were immersed in 10 mM hydrogen peroxide and 10 mM ammonium hydroxide for 30 days. The surface of each specimen was evaluated by profilometry for roughness (Ra) and imaged by scanning electron microscopy. The pH of the biofilm supernatant was significantly higher for the medium containing GlcNAc (p < 0.0001), and was higher in samples containing teeth than the two restorative disks for media containing the same sugar. For both teeth and titanium specimens, the samples treated with glucose-biofilm presented higher roughness values (Ra) than those with GlcNAc-biofilm and every other group. SEM images of the teeth and titanium disks largely supported the profilometry results, with glucose-biofilm samples demonstrating the largest deviation from the reference. For ceramic disks, slightly higher Ra values were obtained for the ammonia group. These findings provide the first direct evidence to support the ability of amino sugars to significantly reduce the cariogenic potential of oral biofilms by altering their biochemistry and bacterial composition. Additionally, amino sugar metabolism appears to be less detrimental to teeth and restorative surfaces than glucose metabolism.

Interpretable machine learning framework reveals microbiome features of oral disease

BACKGROUND

Although the oral microbiome plays an important role in the progression of oral diseases, the microbes closely related to these diseases remain largely uncharacterized.

RESULTS

We collected saliva samples from 140 individuals and performed 16 S amplicon sequencing. An interpretable machine learning framework for imbalanced high-dimensional big data of clinical microbial samples was developed to identify 14 oral microbiome features associated with oral diseases. Microbiome risk scores (MRSs) with the identified features were constructed with SHapley Additive exPlanations (SHAP). Correlations of the MRSs with individual physiological indicators and lifestyle habits were calculated.

CONCLUSION

Our results reveal a set of oral microbiome features associated with oral diseases. Our study demonstrates the feasibility of preventing oral disease through lifestyle interventions and provides a reference method for the era of precision medicine aimed at individualized medicine.

Effects of a combination of fibrolytic and amylolytic enzymes on ruminal enzyme activities, bacterial diversity, blood profile and milk production in dairy cows

We hypothesised that adding a combination of fibrolytic and amylolytic enzymes to the diet of early-lactation dairy cows would improve rumen enzyme activity and bacterial diversity, promote energy metabolism, and benefit milk production in cows. Twenty multiparous early-lactation (90 ± 5 d) Holstein cows with similar body conditions were randomly allocated to control (CON, n = 10) and experimental (EXP, n = 10) groups in a completely randomised single-factor design. The CON was fed only a basal total mixed ration diet, and the diet of the EXP was supplemented with a combination of fibrolytic and amylolytic enzymes at 70 g/cow/d (cellulase 3 500 CU/g, xylanase 2 000 XU/g, β-glucanase 17 500 GU/g, and amylase 37 000 AU/g). The experiment lasted 28 days, with 21 days for adaptation and 7 days for sampling. Enzyme addition increased the activity levels of α-amylase and xylanase, and the ammonia-N concentration (P < 0.05) tended to increase the activity of β-glucanase (P = 0.08) in rumen fluid. However, there was no significant difference in the rumen bacterial richness and diversity, phylum (richness > 0.1%) or genus (richness > 1%) composition between the CON and EXP groups (P > 0.05). A tendency of difference was found between CON and EXP (R = 0.22, P = 0.098) in principal component analysis. Ten genera showed different abundances across the CON and EXP groups (linear discriminant analysis effect size, linear discriminant analysis > 2). EXP increased the ratio of albumin to globulin and the concentrations of total cholesterol and low-density lipoprotein cholesterol (P < 0.05) and tended to increase triglycerides (P = 0.09) in blood. Milk yield, 3.5% fat-corrected milk yield and energy-corrected milk yield increased with enzyme supplementation (P < 0.05). The production levels of milk fat and lactose increased, but the percentage of solids, not fat and protein, decreased in EXP (P < 0.05). Although the DM intake was not affected, the feed efficiency tended to increase (P = 0.07) in EXP. In conclusion, dietary supplementation with a mixture of fibrolytic and amylolytic enzymes on multiparous early-lactation dairy cows increased α-amylase and xylanase activity levels in rumen fluid, enhanced milk performance and tended to improve the feed efficiency in cows.

Maintaining oral health for a hundred years and more? - An analysis of microbial and salivary factors in a cohort of centenarians

Aim

To investigate associations between oral health-related conditions and the oral microbiome in a representative study sample of centenarians.

Materials and methods

Clinical and microbial parameters from 54 centenarians were assessed in the Heidelberg Dental Centenarian Study. Plaque and salivary samples were collected, and the microbiota was characterized by 16S rRNA gene sequencing.

Results

Diversity and structure of the oral microbiome were mainly influenced by the presence of natural teeth and the number of decayed, missing, and filled teeth (0.028 ≤ p ≤ 0.001 in plaque and salivary samples). Centenarians with less caries experience possessed a more diverse oral microbiome. Moreover, the number of dental visits also showed a significant influence on the microbial composition. Most centenarians presented with hyposalivation (mean stimulated flow rate = 0.84 ± 0.55 ml/min), a low buffering capacity, and an acidic pH. The latter was between 5.0 and 5.8 in 46.3% of cases, and we observed that an increased salivary pH correlated with higher alpha-diversity in both salivary and plaque samples.

Conclusion

The microbiome diversity correlated significantly with successful oral aging. In addition, regular dental visits were a beneficial factor. However, diversity can be negatively influenced by hyposalivation, associated with pH changes due to aging effects.

Meta-Analysis Using NGS Data: The Veillonella Species in Dental Caries

Objectives: In light of recent technological advances in Next-generation sequencing (NGS) and the accumulation of large, publicly available oral microbiome datasets, the need for meta-analysing data on caries microbiome is becoming feasible and essential. A consensus on the identification of enriched organisms in cariogenic dysbiotic biofilms would be reached. For example, members of the Veillonella genus have been detected in caries biofilms, and may have an underestimated contribution to the dysbiotic process. Hence, we aimed to determine the abundance of Veillonella species in dental caries in studies using NGS data.

Materials and Methods: Analysis was performed according to the Preferred Reporting Items for Systematic Review and Meta-Analysis (registered at PROSPERO: CRD42020204150). Studies investigating microbial composition in saliva, dental biofilm, or carious dentin were included. Six databases and grey literature were searched. Two independent reviewers selected the papers and assessed the methodological quality.

Results: Searches retrieved 1,323 titles, from which 38 studies were included in a qualitative synthesis, comprising a total of 1,374 caries and 745 caries-free individuals. Most studies analysed 16S rRNA amplicons, and only 5 studies used shotgun metagenomics and metatranscriptomics. A geographical bias was observed. The methodological quality was downrated in 81.5% of the studies due to the lack of criteria for defining cases and standard criteria used for measurement of the condition in a reliable way. Six studies on early childhood caries (ECC) were meta-analysed, confirming a significant enrichment of Veillonella spp. in caries-associated biofilms (but not saliva) when compared to caries-free controls [mean difference: 2.22 (0.54–3.90); p = 0.01].

Conclusions:Veillonella spp. is more abundant in individuals suffering with ECC when compared to caries-free controls (very low evidence certainty), and should be considered for further studies to observe their metabolism in dental caries. There is an urgent need for a consensus in methodologies used to allow for more rigorous comparison between NGS studies, particularly including clinical data and details of caries diagnosis, as they are currently scarce. Inconsistent reporting on the NGS data affected the cross-study comparison and the biological connexions of the relative abundances on caries microbiome.

Metagenomic Analysis of Dental Plaque on Pit and Fissure Sites With and Without Caries Among Adolescents

Caries is one of the most prevalent infectious diseases worldwide and is driven by the dysbiosis of dental biofilms adhering to tooth surfaces. The pits and fissured surfaces are the most susceptible sites of caries. However, information on the taxonomic composition and functional characteristics of the plaque microbiota in the pit and fissure sites is very limited. This study aimed to use metagenomic sequencing analyses to investigate the relationship between the plaque microbiome in the pit and fissure site and caries in adolescents. A total of 20 adolescents with active pit and fissure surface caries were involved as well as 20 age-matched, caries-free teenagers for control tests. Plaque samples were collected from the pit and fissure site and were subjected to metagenomic analyses, in which the microbial communities were investigated. Our results showed that the microbiota diversity was similar between those two groups. At the species level, the relative abundances of A. gerencseriae, P. acidifaciens, P. multisaccharivorax, S. oralis, S. mutans, and P. denticolens were higher in the caries-active group. N. elongata, C. hominis, and A. johnsonii were relatively more abundant in the caries-free groups. Functional analysis suggested that the metabolic pathway was the most abundant pathway, and the functional traits of the level 2 pathways included amino acid metabolism, metabolism of cofactors, and vitamins and carbohydrate metabolism. Our results also revealed that the caries group displayed several alterations in metabolic pathways, including enriched functions in carbohydrate digestion and absorption. This study suggested that in addition to the specific anatomical structures of the pit and fissured surfaces, the fundamental differences in the plaque microbiome may also be related to the susceptibility of pit and fissure caries.

Periodontal Pathogens Inhabit Root Caries Lesions Extending beyond the Gingival Margin: A Next-Generation Sequencing Analysis

We performed a comprehensive microbiome analysis of root caries lesions using 22 teeth extracted from patients with severe periodontitis. The carious lesions were mechanically collected and cryo-pulverized following tooth extraction. Differences in the microbiome were compared between independent lesions at the supragingival site (SG) and lesions extending beyond the gingival margin (GCB). DNA was extracted and the microbiome was characterized on the basis of the V3-V4 hypervariable region of the 16S rRNA gene using paired-end sequencing on an Illumina MiSeq device. The microbiota in root caries lesions showed compositionally distinct microbiota depending on the location. The most abundant OTUs in the SG group were Streptococcus (26.0%), Actinomyces (10.6%), and Prevotella (7.6%). GCB presented Prevotella (11.1%) as the most abundant genus, followed by Fusobacterium (9.6%) and Actinomyces (8.7%). The SG group showed a lack of uniformity in microbiota compared with the GCB group. The bacterial profiles of GCB varied considerably among patients, including periodontal pathogens such as Porphyromonas, Selenomonas, Filifactor, Peptococcus, and Tannerella. Periodontal pathogens inhabit root caries lesions that extend beyond the gingival margin. This study provides a new perspective for elucidating the microbial etiology of root caries.

The impact of caries status on supragingival plaque and salivary microbiome in children with mixed dentition: a cross-sectional survey

Background

Supragingival plaque and saliva are commonly used for microbiome analysis. Many epidemiological studies have identified deciduous teeth caries as a risk factor for caries development in first permanent molar (FPM); nevertheless, to the best of our knowledge, there are no reports on the effects of deciduous teeth caries on the microbiome of healthy FPM. Additionally, it remains unclear whether saliva can be used instead of supragingival plaque for caries microbial studies. Therefore, we aimed to elucidate this issue, and to characterize and compare the oral microbiome of healthy FPMs in children with different caries statuses and that from children with and without caries in a similar microhabitat, by PacBio sequencing. Currently, few studies have investigated the oral microbiome of children using this technique.

Methods

Thirty children (aged 7–9 years) with mixed dentition were enrolled; 15 had dental caries, and 15 did not. Supragingival plaques of deciduous molars and maxillary FPMs, and non-stimulating saliva samples were collected. DNA was extracted and the v1–v9 regions of 16S rRNA were amplified. Subsequently, PacBio sequencing and bioinformatic analyses were performed for microbiome identification.

Results

The microbial alpha diversity of the saliva samples was lower than that of the supragingival plaque (p < 0.05); however, no differences were detected between deciduous teeth and FPMs (p > 0.05). In addition, the alpha and beta diversity of children with and without caries was also similar (p > 0.05). Nonmetric multidimensional scaling and Adonis analyses indicated that the microbial structure of salivary and supragingival plaque samples differ (p < 0.05). Further analysis of deciduous teeth plaque showed that Streptococcus mutans, Propionibacterium acidifaciens, and Veillonella dispar were more abundant in children with caries than in those without (p < 0.05); while in FPMs plaque, Selenomonas noxia was more abundant in healthy children (p < 0.05). No differences in microorganisms abundance were found in the saliva subgroups (p > 0.05).

Conclusion

We have determined that supragingival plaque was the best candidate for studying carious microbiome. Furthermore, S. mutans, V. dispar, and P. acidifaciens were highly associated with deciduous teeth caries. S. noxia may be associated with the abiding health of FPM; however, this requires additional studies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12903-021-01683-0.

Quantification of Bacterial Colonization in Dental Hard Tissues Using Optimized Molecular Biological Methods

Bacterial infections of root canals and the surrounding dental hard tissue are still a challenge due to biofilm formation as well as the complex root canal anatomy. However, current methods for analyzing biofilm formation, bacterial colonization of root canals and dental hard tissue [e.g., scanning electron microscopy, confocal laser scanning microscopy (CLSM) or determination of colony forming units (CFU)] are time-consuming and only offer a selective qualitative or semi-quantitative analysis. The aim of the present study is the establishment of optimized molecular biological methods for DNA-isolation and quantification of bacterial colonization via quantitative PCR (qPCR) from dental hard tissue. Root canals of human premolars were colonized with Enterococcus faecalis. For isolation of DNA, teeth were then grinded with a cryo mill. Since the hard tissues dentin and especially enamel belong to the hardest materials in the human organism, the isolation of bacterial DNA from root dentin is very challenging. Therefore, treatment steps for the isolation of DNA from grinded teeth were systematically analyzed to allow improved recovery of bacterial DNA from dental hard tissues. Starting with the disintegration of the peptidoglycan-layer of bacterial cells, different lysozyme solutions were tested for efficacy. Furthermore, incubation times and concentrations of chelating agents such as EDTA were optimized. These solutions are crucial for the disintegration of teeth and hence improve the accessibility of bacterial DNA. The final step was the determination of prior bacterial colonization of each root canal as determined by qPCR and comparing the results to alternative methods such as CFU. As a result of this study, optimized procedures for bacterial DNA-isolation from teeth were established, which result in an increased recovery rate of bacterial DNA. This method allows a non-selective and straightforward procedure to quantify bacterial colonization from dental hard tissue. It can be easily adapted for other study types such as microbiome studies and for comparable tissues like bones.

Antibacterial effect of a brominated self-etch adhesive on carious dentin - An in vivo study

OBJECTIVES

This in vivo study compared the antibacterial effect of a self-etch adhesive with and without the brominated monomer 12-methacryloyloxydodecyl-pyridinium bromide (MDPB) on carious dentin after selective caries removal.

METHODS

10 patients showing deep primary carious lesions at two posterior teeth without pulpal symptoms were included. At visit I, carious tissue was selectively removed and carious dentin was sampled with a sterile roundbur (Komet No. 18). One cavity was restored with composite (SDR, Ceram X; DENTSPLY DeTrey) using an MDPB-containing self-etch adhesive (Clearfil Protect Bond, Kuraray Noritake; PB). The other restoration served as a control (Clearfil SE Bond II, Kuraray Noritake; SE). At visit II after 8 weeks, carious dentin was sampled again. Bacterial growth in carious dentin was differentiated using microbial cultivation. Bacterial DNA from intact cells and cell-free DNA were quantified using 16S rRNA gene-based real-time PCR and the microbial community composition was analyzed by amplicon deep-sequencing. Wilcoxon test was applied for statistical analysis.

RESULTS

Both treatments showed a decrease of intact bacterial cells in carious dentin at visit II compared to visit I (PB: visit I: 1.1*10⁶, visit II: 1.7*10⁵ (p = 0.03); SE: visit I: 1.1*10⁷, visit II = 2.4*10⁵ (p = 0.002)). No statistically significant reduction of cell-free bacterial DNA was detected (PB: visit I: 6.1*10⁵, visit II: 1.6*10⁵ (p = 0.08); SE: visit I: 5.3*10⁵, visit II: 2.9*10⁵ (p = 0.10)). The decrease of intact cell-derived (p = 0.371) and cell-free DNA (p = 0.455) did not differ significantly between PB and SE. Lactobacillus was most abundant within the microbial community at both visits. Alpha-diversity was not affected by treatment and samples showed high intra- and interindividual diversity.

CONCLUSION AND CLINICAL SIGNIFICANCE

Both self-etch adhesives have an antibacterial effect due to a decrease of bacterial DNA after selective caries removal. However, the results do not reveal any additional antibacterial effect by MDPB. The study is registered with the German Clinical Trials Register (DRKS00011532).

Rubber Dam Isolation and High-Volume Suction Reduce Ultrafine Dental Aerosol Particles: An Experiment in a Simulated Patient

The ongoing Coronavirus Disease 2019 (COVID-19) pandemic has triggered the paralysis of dental services ascribed to the potential spread of severe acute respiratory syndrome (SARS)-CoV-2. Aerosol-generating procedures (AGPs) are common in dentistry, which in turn increase the risk of infection of the dental personnel due to the salivary presence of SARS-CoV-2 in COVID-19 patients. The use of rubber dam isolation (RDI) and high-volume evacuators (HVE) during AGPs is recommended to control dental aerosols, but the evidence about their effectiveness is scarce. This first study aimed to compare, in a simulated patient, the effectiveness of the following strategies: standard suction (SS), RDI and RDI + HVE. Using the laser diffraction technique, the effect of each condition on the volume distribution, average size and concentration of coarse (PM10), fine (PM2.5) and ultrafine (PM0.1) particles were evaluated. During the teeth drilling, the highest volume fraction of dental aerosol particles with SS was below 1 μm of aerodynamic diameter. Additionally, the RDI + HVE significantly reduced both the ultrafine dental aerosol particles and the concentration of total particulate matter. AGPs represent a potential risk for airborne infections in dentistry. Taken together, these preliminary results suggest that isolation and high-volume suction are effective to reduce ultrafine dental aerosol particles.

Annual review of selected scientific literature: A report of the Committee on Scientific Investigation of the American Academy of Restorative Dentistry

This comprehensive review of the 2019 restorative dental literature is offered to inform busy dentists regarding remarkable publications and noteworthy progress made in the profession. Developed by the Scientific Investigation Committee of the American Academy of Restorative Dentistry, each author brings discipline-specific expertise to 1 of 8 sections of the report: (1) prosthodontics; (2) periodontics, alveolar bone, and peri-implant tissues; (3) implant dentistry; (4) dental materials and therapeutics; (5) occlusion and temporomandibular disorders; (6) sleep-related breathing disorders; (7) oral medicine and oral and maxillofacial surgery; and (8) dental caries and cariology. The report targets important information likely to influence day-to-day dental treatment decisions. Each review is not intended to stand alone but to update interested readers so that they may visit source material when greater detail is desired. As the profession moves toward evidence-based clinical decision-making, an incredible volume of potentially valuable dental literature continues to increase. It is the intention of this review and its authors to provide assistance in negotiating the extensive dental literature published in 2019. It is our hope that readers find this work useful in the clinical management of dental patients.

Effects of dihydroartemisinin on the gut microbiome of mice

Dihydroartemisinin (DHA) is a semisynthetic derivative of artemisinin, which has been found to exhibit a broad range of biological activities, excluding antimalarial effects; however its effects on the gut microbiota remain poorly understood. The present study aimed to investigate the effects of DHA on the gut microbiome in mice and to determine its potential biological and pharmaceutical activities through its alteration of the gut microbiota. Serum glucose, triglyceride (TG), total cholesterol, lipopolysaccharide, high density lipoprotein‑cholesterol, low density lipoprotein‑cholesterol, alanine aminotransferase and aspartate aminotransferase levels in mice treated with DHA were analyzed using the corresponding detection kits. In addition, hematoxylin and eosin staining was performed to determine the pathological effects of DHA on the liver, kidney and intestinal tissues of mice, and the effects of DHA on the gut microbiome were analyzed using 16S ribosomal (r)DNA gene analysis. The results demonstrated that the TG serum levels of mice treated with DHA were significantly decreased compared with the control group. Furthermore, 16S rDNA gene analysis demonstrated that the bacterial diversity of mice treated with DHA was enriched compared with the control group. The DHA group exhibited increased numbers of Firmicutes and Saccharibacteria, and decreased Deferribacteres and Actinobacteria compared with the control group at the phylum level. Kyoto Encyclopedia of Genes and Genomes signaling pathway enrichment analysis also revealed that the signaling pathways associated with 'Energy metabolism' and 'Nucleotide metabolism' were upregulated, whereas the signaling pathways associated with 'Infectious diseases and 'Neurodegenerative diseases' were downregulated in the DHA group compared with the control group. In conclusion, the findings of the present study indicated that DHA may significantly decrease the serum TG levels and alter the gut microbiota, which suggested its potential to be used for the treatment of hyperlipidemia, inflammatory and neurodegenerative disorders.

Effect of a bioactive cement on the microbial community in carious dentin after selective caries removal - An in-vivo study

OBJECTIVES

Selective caries removal in deep lesions means that soft carious affected dentin is left in the center of the cavity. Thus, using a tricalcium silicate cement Biodentine™ (Septodont, Paris) to seal the remaining soft dentin could have an antibacterial effect. This in-vivo study aimed to do quantitative and qualitative analyses on the bacterial composition within carious dentin before and after selective caries removal when applying Biodentine.

METHODS

Eleven patients with deep primary carious lesions at two posterior teeth without pulpal symptoms were included. Carious dentin was selectively removed and sampled with a sterile round bur (Komet No. 18) at baseline visit and eight weeks later. On the first visit, one lesion per patient, the remaining carious dentin was covered with Biodentine before adhesive restoration. Caries samples were investigated by microbial cultivation, molecular analysis and amplicon deep-sequencing of 16S rRNA genes. Bacterial DNA from intact cells was differentiated from cell-free DNA by DNase degradation prior to DNA isolation.

RESULTS

Reduction of cell-derived as well as cell-free bacterial DNA eight weeks after selective caries removal was significantly higher when Biodentine was applied. Lactobacillus was most abundant within the microbial community of deep carious dentin lesions at the first visit. After intervention with Biodentine application, Lactobacillus was diminished to a high degree. In general, the diversity in samples, as well as bacterial composition differed interindividually as well as intraindividually.

CONCLUSION AND CLINICAL SIGNIFICANCE

Despite the heterogenous and diversity of microbial composition in patients, Biodentine can have beneficial antibacterial effects when applied to residual carious dentin, offering an alternative and safe treatment option. The study is officially registered with German Clinical Trials Register (DRKS00011067).